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Hierarchical Organisation and the 3D Toolbox

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1.      The mammalian genome is organised into a complex hierarchy:

1.      The mammalian genome is organised into a complex hierarchy: topics

Hierarchy includes 1,2,3
    Examples

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1.      To study this architecture researchers use a specialised toolbox

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1.      Dna accessibility

1.      Dna accessibility topics

Name of tool 1 – dhss
    mechanism
    Function
    Name of tool 2 – atac seq
    Mechanism
    Function

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1.      3d mapping:

1.      3d mapping: topics

Tool 1 – 3c
    Function
    Tool 2 – 4c
    Function
    Tool 3 – hic
    Function
    Tool 4 – capture c
    Function

1.      The mammalian genome is organised into a complex hierarchy: Hierarchy includes 1,2,3

primary DNA sequence, secondary nucleosome structures, and tertiary 3D architecture

1.      The mammalian genome is organised into a complex hierarchy: Examples

chromatin loops, Topologically Associating Domains (TADs), A/B compartments, and chromosome territories

1.      Dna accessibility Name of tool 1 –

dhss

1.      Dna accessibility dhss mechanism

mark regions where nucleosomes are absent,

1.      Dna accessibility dhss Function

identifying promoters and enhancers.

1.      Dna accessibility Name of tool 2 –

atac seq

1.      Dna accessibility atac seq Mechanism

uses a Tn5 transposase to fragment and tag accessible DNA,

1.      Dna accessibility atac seq Function

measuring nucleosome positioning.

1.      3d mapping: Tool 1 –

3c

1.      3d mapping: 3c Function

measures one-to-one interactions

1.      3d mapping: Tool 2 –

4c

1.      3d mapping: 4c Function

maps unknown regions interacting with a viewpoint (one-to-many)

1.      3d mapping: Tool 3 –

hic

1.      3d mapping: hic Function

provides a genome-wide interaction matrix (all-to-all);

1.      3d mapping: Tool 4 –

capture c

1.      3d mapping: capture c Function

offers high-resolution mapping of specific regio